ArticleGenome biology2011
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers, 1 of them a synthesis that pooled it.
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Who cites it
160 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Rare Exome Sequence Variants in CLCN6 Reduce Blood Pressure Levels and Hypertension Risk.Circulation. Cardiovascular genetics · 2016Pooled it
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- Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping inInternational journal of molecular sciences · 2024Article
- HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data.Nucleic acids research · 2024Article
- Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species.Nucleic acids research · 2023Article
- Dominant negative variants in KIF5B cause osteogenesis imperfecta via down regulation of mTOR signaling.PLoS genetics · 2023Article
- Mitochondrial heteroplasmic shifts reveal a positive selection of breast cancer.Journal of translational medicine · 2023Article
- Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality.Nature communications · 2023Article
- Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease.American journal of human genetics · 2023Article
- The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle.Genetics, selection, evolution : GSE · 2023Article
- Evaluating the Transition from Targeted to Exome Sequencing: A Guide for Clinical Laboratories.International journal of molecular sciences · 2023Article
100 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
backgroundEnrichment of loci by DNA hybridization-capture, followed by high-throughput sequencing, is an important tool in modern genetics. Currently, the most common targets for enrichment are the protein coding exons represented by the consensus coding DNA sequence (CCDS). The CCDS, however, excludes many actual or computationally predicted coding exons present in other databases, such as RefSeq and Vega, and non-coding functional elements such as untranslated and regulatory regions. The number of variants per base pair (variant density) and our ability to interrogate regions outside of the CCDS regions is consequently less well understood.
resultsWe examine capture sequence data from outside of the CCDS regions and find that extremes of GC content that are present in different subregions of the genome can reduce the local capture sequence coverage to less than 50% relative to the CCDS. This effect is due to biases inherent in both the Illumina and SOLiD sequencing platforms that are exacerbated by the capture process. Interestingly, for two subregion types, microRNA and predicted exons, the capture process yields higher than expected coverage when compared to whole genome sequencing. Lastly, we examine the variation present in non-CCDS regions and find that predicted exons, as well as exonic regions specific to RefSeq and Vega, show much higher variant densities than the CCDS.
conclusionsWe show that regions outside of the CCDS perform less efficiently in capture sequence experiments. Further, we show that the variant density in computationally predicted exons is more than 2.5-times higher than that observed in the CCDS.
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